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- PDB-5xqj: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Pe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xqj | |||||||||
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Title | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose | |||||||||
![]() | Pcrglx protein | |||||||||
![]() | LYASE / exo-rhamnogalacturonan lyase / enzyme / pectin / SAD / Se | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kunishige, Y. / Iwai, M. / Tada, T. / Nishimura, S. / Sakamoto, T. | |||||||||
![]() | ![]() Title: Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26 Authors: Kunishige, Y. / Iwai, M. / Nakazawa, M. / Ueda, M. / Tada, T. / Nishimura, S. / Sakamoto, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 230.5 KB | Display | |
Data in CIF | ![]() | 321.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xq3SC ![]() 5xqgC ![]() 5xqoC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 100681.797 Da / Num. of mol.: 8 / Fragment: UNP residues 22-927 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.3M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→171.17 Å / Num. obs: 255645 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 6.57 / Num. unique obs: 12654 / CC1/2: 0.974 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XQ3 Resolution: 2.75→171.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.858 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.952 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→171.17 Å
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Refine LS restraints |
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